Abstract The goals of this research are the development of more accurate methods for molecular simulations of solvated proteins, the construction of multiscale kinetic network models which fully exploit this information, and the application of these new computational tools to forefront problems in structural biology and molecular biophysics. These problems include: (a) protein-ligand binding, both thermodynamics and kinetics; and (b) characterizing the landscapes for protein folding and functional transitions in the native state, with emphasis on mapping the diversity of pathways for folding and binding and their corresponding fluxes. We will continue our productive collaboration with the Arnold Group on the design of inhibitors to HIV R; and pursue new collaborations we have started with the Kalodimos group on the recognition of signal sequence peptides upon binding by translocase, and with the Gilson group on the computational framework for modeling binding affinities of host-guest systems. These projects will build on the substantial progress made during the current grant period on the development of state-of-the-art methods for molecular simulations using all atom and multiscale kinetic network models.